Package picard.arrays.illumina
Class IlluminaManifestRecord
- java.lang.Object
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- picard.arrays.illumina.IlluminaManifestRecord
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- Direct Known Subclasses:
Build37ExtendedIlluminaManifestRecord
public class IlluminaManifestRecord extends Object
A class to represent a record (line) from an Illumina Manifest [Assay] entry
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Nested Class Summary
Nested Classes Modifier and Type Class Description protected static class
IlluminaManifestRecord.IlluminaStrand
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Field Summary
Fields Modifier and Type Field Description static String
ILLUMINA_FLAGGED_BAD_CHR
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description String
getAddressAId()
String
getAddressBId()
String
getAlleleAProbeSeq()
String
getAlleleBProbeSeq()
int
getBeadSetId()
String
getChr()
String
getExpClusters()
String
getGenomeBuild()
String
getHgGenomeBuild()
String
getIlmnId()
IlluminaManifestRecord.IlluminaStrand
getIlmnStrand()
int
getIndex()
boolean
getIntensityOnly()
String
getLine()
String
getMajorGenomeBuild()
String
getName()
String
getPloidy()
int
getPosition()
htsjdk.tribble.annotation.Strand
getRefStrand()
String
getSnp()
String
getSource()
String
getSourceSeq()
IlluminaManifestRecord.IlluminaStrand
getSourceStrand()
String
getSourceVersion()
String
getSpecies()
String
getTopGenomicSeq()
boolean
isAmbiguous()
boolean
isIndel()
boolean
isSnp()
void
setHgGenomeBuild(String hgGenomeBuild)
String
toString()
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Field Detail
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ILLUMINA_FLAGGED_BAD_CHR
public static final String ILLUMINA_FLAGGED_BAD_CHR
- See Also:
- Constant Field Values
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Method Detail
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getLine
public String getLine()
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getIlmnId
public String getIlmnId()
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getName
public String getName()
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getIlmnStrand
public IlluminaManifestRecord.IlluminaStrand getIlmnStrand()
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getSnp
public String getSnp()
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isIndel
public boolean isIndel()
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isAmbiguous
public boolean isAmbiguous()
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isSnp
public boolean isSnp()
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getAddressAId
public String getAddressAId()
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getAlleleAProbeSeq
public String getAlleleAProbeSeq()
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getAddressBId
public String getAddressBId()
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getAlleleBProbeSeq
public String getAlleleBProbeSeq()
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getGenomeBuild
public String getGenomeBuild()
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getMajorGenomeBuild
public String getMajorGenomeBuild()
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getHgGenomeBuild
public String getHgGenomeBuild()
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setHgGenomeBuild
public void setHgGenomeBuild(String hgGenomeBuild)
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getChr
public String getChr()
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getPosition
public int getPosition()
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getPloidy
public String getPloidy()
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getSpecies
public String getSpecies()
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getSource
public String getSource()
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getSourceVersion
public String getSourceVersion()
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getSourceStrand
public IlluminaManifestRecord.IlluminaStrand getSourceStrand()
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getSourceSeq
public String getSourceSeq()
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getTopGenomicSeq
public String getTopGenomicSeq()
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getBeadSetId
public int getBeadSetId()
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getExpClusters
public String getExpClusters()
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getRefStrand
public htsjdk.tribble.annotation.Strand getRefStrand()
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getIntensityOnly
public boolean getIntensityOnly()
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getIndex
public int getIndex()
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